Contacts of the strand formed by residues 68 - 75 (chain A) in PDB entry 6OE7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A CYS 4.7 0.4 + - - -
20A TYR* 2.8 59.4 + - + +
21A GLN 4.9 2.6 + - - +
30A PRO* 3.5 12.3 - - + +
31A GLU* 3.4 18.7 + - - +
53A LEU* 4.2 9.6 - - + +
54A LEU 3.5 6.3 - - - +
56A ARG* 5.0 1.4 - - - +
66A SER 4.0 5.1 + - - +
67A GLU* 1.3 80.3 - - - +
69A ILE* 1.3 67.1 - - - +
220A GLU* 2.6 31.1 + - - -
223A VAL* 3.7 18.8 - - - +
224A SER* 2.9 26.9 + - - +
227A LEU* 3.3 27.3 - - + +
302A EDO 3.5 19.0 + - - -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO* 4.2 2.2 - - - -
31A GLU* 3.3 22.2 - - + +
33A ARG* 3.6 45.3 - - + +
53A LEU* 3.3 6.9 - - - +
54A LEU* 2.8 53.3 + - + +
56A ARG* 3.8 31.9 - - + +
59A PHE* 3.9 24.0 - - + -
68A ARG* 1.3 74.7 - - - +
70A ILE* 1.3 70.7 + - - +
71A ALA* 4.4 1.3 - - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.0 12.3 - - + -
15A THR* 5.0 3.1 - - - +
18A CYS* 4.3 10.8 - - - -
30A PRO* 4.0 17.0 - - + +
31A GLU 2.8 15.1 + - - +
32A TRP* 3.2 54.5 - - + +
33A ARG 3.0 24.6 + - - +
51A PRO* 4.1 7.0 - - + -
52A VAL 3.4 9.9 - - - +
53A LEU* 3.9 10.8 - - + -
69A ILE* 1.3 73.9 - - - +
71A ALA* 1.3 63.7 + - - +
121A LEU* 3.7 25.4 - - + -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 4.7 0.2 - - - -
33A ARG* 3.6 20.9 - - + +
34A ASP* 5.8 1.1 - - + -
50A SER 3.6 0.2 - - - +
51A PRO* 4.0 3.1 - - - -
52A VAL* 2.8 37.4 + - - +
54A LEU* 4.3 16.4 - - + -
59A PHE* 5.2 5.4 - - + -
69A ILE* 4.4 1.1 - - + -
70A ILE* 1.3 76.1 - - - +
72A PRO* 1.3 76.4 - - + +
73A MET* 3.6 7.9 + - + -
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 3.7 12.8 - - + -
33A ARG 3.3 15.7 - - - +
34A ASP* 3.3 24.6 - - + +
37A LYS* 3.7 25.4 - - + +
38A TYR* 3.7 23.8 - - + +
49A ASN* 4.2 9.2 - - + -
50A SER 3.4 11.0 - - - +
51A PRO* 4.2 2.7 - - + -
71A ALA* 1.3 87.1 - - + +
73A MET* 1.3 65.8 + - - +
193A TYR* 4.9 0.9 - - - +
303A EDO 4.0 12.6 + - - -
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Residues in contact with MET 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASN* 3.2 6.5 - - - -
50A SER 3.0 29.0 + - - +
52A VAL* 3.5 30.5 - - + -
54A LEU* 3.6 32.3 - - + -
59A PHE* 5.6 0.7 - - + -
71A ALA* 4.3 5.6 - - + +
72A PRO* 1.3 79.3 - - - +
74A ARG* 1.3 63.8 + - - +
118A CYS* 5.1 0.2 - - - -
180A PHE* 3.7 31.9 - - + -
193A TYR* 3.5 40.8 - - + +
194A SER 4.4 3.4 - - - +
195A TYR* 3.4 22.3 - - + -
303A EDO 4.1 1.8 - - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN* 3.3 56.5 + - - +
48A SER 3.6 0.9 - - - -
49A ASN* 3.4 14.1 + - - +
73A MET* 1.3 71.3 - - - +
75A TRP* 1.3 65.9 + - - +
76A GLY* 3.3 14.8 + - - -
78A VAL* 4.3 1.8 - - - +
86A ASP* 5.9 0.2 + - - -
87A PRO* 3.8 27.7 + - - +
88A SER* 4.3 16.0 - - - +
192A LEU* 3.8 34.1 - - + -
193A TYR 2.9 14.9 + - - +
194A SER* 3.1 5.9 - - - -
195A TYR* 2.9 26.8 + - - -
303A EDO 4.0 0.8 - - - +
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Residues in contact with TRP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A CYS 3.4 20.2 - - - -
3A GLY* 3.5 21.1 - - - -
4A ARG* 3.5 5.4 - - - -
5A THR* 4.0 20.0 - - + -
44A LYS* 3.5 26.7 - - + -
45A SER 3.5 5.4 - - - +
46A PRO* 3.4 29.9 - - + +
47A GLN* 2.7 31.2 + - - +
48A SER* 2.8 21.8 + - - +
50A SER* 5.2 0.9 - - - -
73A MET 3.6 1.4 + - - -
74A ARG* 1.3 69.7 + - - +
76A GLY* 1.3 63.8 + - - +
95A THR* 3.2 35.3 + - + +
195A TYR* 3.4 41.3 - + - +
197A ILE* 3.6 23.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il